Urbanization modifies ecosystem conditions and evolutionary processes. This includes air pollution, mostly as tropospheric ozone (O3), which contributes to the decline of urban and peri-urban forests. A notable case are fir(Abies religiosa) forests in the peripheral mountains southwest of Mexico City, which have been severely affected by O3 pollution since the 1970s. Interestingly, some young individuals exhibiting minimal O3—related damage have been observed within a zone of significant O3 exposure. Using this setting as a natural experiment, we compared asymptomatic and symptomatic individuals of similar age (≤15 years old; n = 10) using histological, metabolomic and transcriptomic approaches. Plants were sampled during days of high (170 ppb) and moderate (87 ppb) O3 concentration. Given that there have been reforestation efforts in the region, with plants from different source populations, we first confirmed that all analysed individuals clustered within the local genetic group when compared to a species-wide panel (Admixture analysis with ~1.5K SNPs). We observed thicker epidermis and more collapsed cells in the palisade parenchyma of needles from symptomatic individuals than from their asymptomatic counterparts, with differences increasing with needle age. Furthermore, symptomatic individuals exhibited lower concentrations of various terpenes (ß-pinene, ß-caryophylene oxide, α-caryophylene and ß-α-cubebene) than asymptomatic trees, as evidenced through GC-MS. Finally, transcriptomic analyses revealed differential expression for thirteen genes related to carbohydrate metabolism, plant defense, and gene regulation. Our results indicate a rapid and contrasting phenotypic response among trees, likely influenced by standing genetic variation and/or plastic mechanisms. They open the door to future evolutionary studies for understanding how O3 tolerance develops in urban environments, and how this knowledge could contribute to forest restoration.

Many social insect species build nests, which strongly differ from the surrounding environment and are often occupied by specific organismal communities. In temperate forests, red wood ants (e.g. Formica polyctena) are known to create such distinct, highly developed nests, which consist of large, above-ground mounds. Those structures are built primarily out of plant matter collected from the forest litter. Common fungal dwellers of forest litter are representatives of Mucoromycota, engaged in the decomposition process of this substrate. However, data on co-occurrence or interactions between these ants and fungi remains unknown. In order to elucidate these interactions we characterized Mucoromycota communities of Formica polyctena nests and the surrounding forest litter. We sampled four sites, twice in a season and used: a culturomics approach, complemented with DNA barcoding to describe fungal communities; PERMANOVA test and non-metric multidimensional scaling ordinations to compare those communities; and multilevel pattern analysis to indicate taxa associated with the mounds. Our results show that the Mucoromycota community of Formica polyctena’s mound is specific and more stable than the community of the surrounding forest litter. While representatives of Entomortierella lignicola and Absidia cylindrospora clade were found to be associated with the mound environment, representatives of Umbelopsis curvata and Podila verticillata-humilis clade were associated with forest litter, and were rarely present in the mounds. Our findings strongly suggest that the red wood ants’ nest is a specific microenvironment in the temperate forest floor, which is a preferred microhabitat for the mound-associated Mucoromycota, possibly adapted to live in close proximity to ants.

Invasive omnivores may have profound impacts on ecological communities through diet selection, particularly when their functional roles differ from those in their native range. While the threat of feral pigs (Sus scrofa) to native plant communities in Hawai‘i are well known, their trophic dynamics and the drivers of variation in their diet remain understudied. We investigated the feral pig dietary niche on Hawai‘i Island using stable isotopes (13C and 15N) and Bayesian mixing models to identify drivers of variation in resource use. We also chronologically reconstructed diets for six subsampled individuals to understand temporal variation in resource use and individual diet specialization. Our results revealed feral pigs on Hawai‘i Island exhibit a broad dietary niche characterized by diverse diets, with substantial overlap in resource use across districts and habitats. Differences in dietary composition in the transition from forest to open habitat were driven primarily by an increasing reliance on human food subsidies in conjunction with a decreasing reliance on invertebrates, which may be partially driven by protein constraints on dietary composition. Pigs in forested areas largely displayed generalist feeding strategies, while those in open habitat tended to specialize, particularly on human food resources. Diets for chronologically subsampled individuals varied little, suggesting feral pig resource-use strategies in Hawai‘i tend to be stable through time. Individual niche-width was relatively narrow compared to that of feral pigs in Hawai‘i at large, indicating the relatively wide feral pig dietary niche is characterized by substantial intraspecific diet specialization, likely as a result of strong intraspecific competition. Understanding the drivers of feral pig resource use is crucial for informing management strategies aimed at mitigating their ecological impacts in imperiled systems like Hawai‘i.

The oceanographic conditions of the Southern California Bight (SCB) dictate the distribution and abundance of prey resources and therefore the presence of mobile predators, such as Cuvier’s beaked whales (Ziphius cavirostris). Cuvier’s beaked whales are deep-diving odontocetes that spend a majority of their time foraging at depth. Due to their cryptic behavior, little is known about how they respond to seasonal and interannual changes in their environment. This study utilizes passive acoustic data recorded from two sites within the SCB to explore the oceanographic conditions that Cuvier’s beaked whales appear to favor. Utilizing optimum multiparameter analysis, modeled temperature and salinity data are used to identify and quantify these source waters: Pacific Subarctic Upper Water (PSUW), Pacific Equatorial Water (PEW), and Eastern North Pacific Central Water (ENPCW). The interannual and seasonal variability in Cuvier’s beaked whale presence was related to the variability in El Niño Southern Oscillation events and the fraction and vertical distribution of the three source waters. Cuvier’s beaked whale acoustic presence was highest during the winter and spring and decreased during the late summer and early fall. These seasonal increases occurred at times of increased fractions of PEW in the California Undercurrent and decreased fractions of ENPCW in surface waters. Interannual increases in Cuvier’s beaked whale presence occurred during El Niño events. These results establish a baseline understanding of the oceanographic characteristics that correlate with Cuvier’s beaked whale presence in the SCB. Furthering our knowledge of this elusive species is key to understanding how anthropogenic activities impact Cuvier’s beaked whales.

Globally, biodiversity is at risk of extinction, and megadiverse countries become key targets for conservation. South Africa, the only country hosting three biodiversity hotspots, harbours tremendous diversity of at-risk species deserving to be protected. However, the lengthy risk assessment process and the lack of required data to complete assessments is a serious limitation to conservation since several species may slide into extinction while awaiting risk assessment. Here, we employed deep neural network model integrating species climatic and geographic features to predict the conservation status of 116 unassessed plant species. Our analysis involved in total 1072 plant species and 112 066 occurrence points. The best-performing model exhibits high accuracy, reaching up to 83.6% at the binary classification and 56.8% at the detailed classification. Our best-performing model predicts that 32% and 8% of Data Deficient and Not-Evaluated species are likely threatened, respectively, amounting to a proportion of 24.1% of unassessed species facing a risk of extinction. Interestingly, all unassessed species predicted to be threatened are in protected areas, revealing the effectiveness of the South Africa’s network of protected areas in conservation, although these likely threatened species are more abundant outside protected areas. Considering the limitation in assessing only species with available data, there remains a possibility of a higher proportion of unassessed species being imperiled.

The genus Encephalartos is entirely endemic to Africa. Like most cycad species, the genus is at risk of extinction. One of the threats jeopardizing the future of the genus is reproduction failure. Our objective is to investigate what predisposes Encephalartos species to reproduction failure. We collected functional traits of 430 individuals of Encephalartos villosus, including pre-dispersal seed predation and habitat types and elevation in Origi Gorge Nature Reserve in South Africa. Then, we analysed our data by fitting a structural equation model (SEM). Surprisingly, elevation does not predict pre-dispersal seed predations, adding to the inconsistent effects of elevation on seed predation. However, there was evidence of more predated seeds on plants with more leaves, fitting the patterns of resource concentration hypothesis which predicts more insect herbivores, particularly specialist herbivores, where food resources (e.g., leaves, flowers, fruits, and seeds) are abundant. We also found that more predated seeds are in open habitats, perhaps mirroring the specialist feeding behaviour of the weevil Antliarhinus zamiae feeding on the seeds of Encephalartos spp. Furthermore, taller plants tend to bear more predated seeds, potentially because taller plants are easy located by the weevil. Finally, large canopy correlates negatively with predated seeds, mirroring our finding of increased seed predation in open habitats. Our SEM explains 67% of the variations in pre-dispersal seed predations, suggesting that this metamodel provides insights into the predisposition of cycad seed to predations. Since open habitats correlate with more seed predation, we suggest that anthropogenic activities that contribute to open forest must be avoided if we are to limit seed predations.

The importance of scale when investigating ecological patterns and processes is recognised across many species. In marine ecosystems, the processes that drive species distribution have a hierarchical structure over multiple nested spatial and temporal scales. Hence, multi-scale approaches should be considered when developing accurate distribution models to identify key habitats, particularly for populations of conservation concern. Here, we propose a modelling procedure to identify the best spatial and temporal scale for each modelled and remotely sensed oceanographic variable to model harbour porpoise (Phocoena phocoena) distribution. Harbour porpoise sightings were recorded during dedicated line-transect aerial surveys conducted in the summer of 2016, 2021 and 2022 in the northeast Atlantic. Binary generalised additive models were used to assess the relationships between porpoise presence and oceanographic variables at different spatial (5, 20 and 40 km) and temporal (daily, monthly and across survey period) scales. Selected variables included sea surface temperature, thermal fronts, chlorophyll-a, sea surface height, mixed layer depth and salinity. A total of 30,514 km was covered on-effort with 216 harbour porpoise sightings recorded. Overall, the best spatial scale corresponded to the coarsest resolution considered in this study (40 km), while porpoise presence showed stronger association with oceanographic variables summarised at a longer temporal scale (monthly and averaged over survey period). Habitat models including covariates at coarse spatial and temporal scales may better reflect the processes driving availability and abundance of prey resources at the large scales covered during the surveys. These findings support the hypothesis that a multi-scale approach should be applied when investigating species distribution. Identifying suitable spatial and temporal scale would improve the functional interpretation of the underlying relationships, particularly when studying how a small marine predator interacts with its environment and responds to climate and ecosystem changes.

Globally, hammerhead sharks have experienced severe declines owing to continued overexploitation and anthropogenic change. The smooth hammerhead shark Sphyrna zygaena remains comparatively understudied compared to other members of the family Sphyrnidae, and despite its Vulnerable status, a comprehensive understanding of its genetic landscape remains lacking. The present study aimed to conduct a fine-scale genomic assessment of Sphyrna zygaena within the highly dynamic marine environment of South Africa’s coastline, using thousands of single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (3RAD). A combination of differentiation-based outlier detection methods (OUTFlank and pcadapt) and Genotype-Environment Association (GEA) (Redundancy Analysis) analysis in Sphyrna zygaena were employed. Subsequent assessments of putatively adaptive loci revealed a distinctive south to east genetic cline. Amongst these, notable correlations between adaptive variation and sea-surface dissolved oxygen and salinity, in addition to spatial factors were evident. Conversely, analysis of 110, 965 neutral SNP markers revealed a lack of regional population differentiation, a finding that remained consistent across various analytical approaches, including an assessment of isolation-by-distance (IBD) and isolation-by-environment (IBE), genetic clustering analyses (LEA, fastSTRUCTURE, and find.clusters), and a discriminant analysis of principal components (DAPC). These results provide evidence for the presence of differential selection pressures within a limited spatial range, despite high gene flow implied by the selectively neutral dataset. This study offers notable insights regarding the potential impacts of genomic variation in response to fluctuating environmental conditions in the circumglobally distributed Sphyrna zygaena.

Ireland and Britain are two islands located at Europe’s westernmost edge, both of which act as the final breeding outposts for many bird species within their European ranges. Despite their similar geographic locations and geological histories, Ireland and Britain host different breeding avifauna assemblages. Diversity profiles, which can serve as more robust alternatives to classic diversity indices, were employed in this study to explore disparities in the two islands’ breeding avifauna assemblages. Variations in assemblages were explored, along with their potential drivers, through analyses at three levels: island-scale breeding bird assemblage compositions, island-scale diversity profiles considering 49 common breeding species, and habitat-specific diversity profiles considering assemblages in east/central Irish farmland and East Anglian farmland. Analysis of the two islands’ breeding avifauna assemblages revealed that the Irish assemblage is a complete subset of the British assemblage. Analyses of Irish and British assemblages at both an island scale and a habitat scale revealed patterns linking land use to trends within the two islands’ avifauna assemblages. Irish assemblages contained greater proportions of insectivorous farmland species by abundance, while British assemblages contained greater proportions of seed-eating farmland species; both trends appeared to be related to structural differences in agricultural land use on the two islands. The British and East Anglian assemblages exhibited higher diversity across all analyses, which appeared to be driven by the assemblages’ higher relative abundances of species that were most genetically distinct. This study highlights the ability of diversity profiles to impart more information than classic diversity indices by incorporating species similarity data.

1. Fucoid forests are areas dominated by marine brown seaweed in the taxonomic order Fucales that, like the better-known marine foundation species - corals, kelps, seagrasses, salt marshes, and mangroves - are threatened by anthropogenic stressors. 2. Fucoid forests are fabulous and important because they, like the better-known marine foundation species (i) span large areas, bioregions, and ecosystems, (ii) provide ecological functions such as high productivity and biodiversity, and (iii) support a variety of ecosystem services including habitat for commercial fishery species, food for humans and cultural values. 3. Fucoid forests are, based on a new citation analysis, forgotten worldwide, because they are described orders of magnitude less than the better-known marine foundation species, in ecology and marine biology textbooks, in Google Scholar and Scopus databases over scientific literature, and in recent reports and reviews about seaweed forests. 4. Fucoid forests would be less forgotten if more people acknowledge their biological importance and societal value more often and equate their importance to that of the better-known marine foundation species. Perhaps name-recognition would also improve if fucoids are unified under a non-taxonomic common name across teaching, research, management, and conservation, like the better-known marine foundation species. We agree with the marine scientists that have used ‘rockweed’ as such a common name to describe all fucoids, but other seaweed-experts disagree because they (a) do not agree fucoids are forgotten, (b) dislike common names or (c) argue rockweed should only describe fucoid species in the family Fucaceae.

The relationships among developmental stability, canalization and phenotypic plasticity are not straightforward, but may be better understood in the context of temporally heterogeneous environments. Our objective was to investigate the effects of early experience with temporally heterogeneous water availability on the associations between developmental stability, canalization and phenotypic plasticity. We subjected eight plant species to a first round of alternating inundation and drought vs. constantly moderate water treatments and a second round of water conditions. Fluctuating asymmetry (FA), intra- and inter-individual variation (CVintra and CVinter), and plasticity in traits were measured and correlations between variables were calculated for each species. Early temporally heterogeneous experience decreased the leaf size of half of the species, but had complex effects on leaf fluctuating asymmetry (FA) and inter-individual variation (CVinter) in traits immediately or in late conditions, with little effects on intra-individual variation (CVintra). There were several positive correlations between FA and CVinter, positive correlations between CVinter and plasticity in early treatments, but negative correlations in late treatments. Our results suggested complexity and variability in the relationships between different mechanisms. Decreased canalization may promote plastic responses in traits before or during the induction of plasticity, whereas canalization may reflect phenotypic convergence after plastic responses. Temporally heterogeneous experiences may facilitate positive correlations or attenuate negative correlations between decreased canalization and plasticity. We provide direct evidence for relationships between developmental stability, canalization and plasticity as well as the role of temporally heterogeneous environments in modifying these processes. The integrative way that plants deal with environmental variation demonstrates their ability to evolve in multiple directions via many flexible adjustments in response to varying environmental signals over a plant’s lifetime.

The foraging strategies of sympatric ungulates with similar ecological niches are important for understanding ecological niche differentiation, resource utilization, competition, and coexistence and for understanding the ecological impacts on plant communities in the ecosystem. The behavior of the wapiti (Cervus elaphus) and Siberian roe deer (Capreolus pygargus) foraging on Japanese yew (Taxus cuspidata) has affected its succession and renewal in the northeastern forests of China, which has become an urgent problem for the relevant departments. This study analyzed the foraging strategies of the wapiti and Siberian roe deer on Japanese yew from July 2021 to January 2024 using field investigations and infrared camera monitoring in the Muling National Nature Reserve, Heilongjiang Province, China. It was found that the wapiti and Siberian roe deer have different foraging strategies in terms of time, space, and behavior. Temporally, they both preferred to forage for the saplings of the Japanese yew during the winter season, the degree of overlap in foraging rhythms was medium (Dhat1=0.67), and the diurnal foraging activity index (DRAI) of the wapiti was larger than that of the Siberian roe deer. Spatially, the suitable foraging habitat of the Siberian roe deer was twice that of the wapiti, and their overlap was low in the location and direction of saplings and the distance of the seed tree. Behaviorally, the foraging intensity of the wapiti was heavy, and Siberian roe deer was low. Foraging reduced the average primary branch height, number of new branches, and length of lateral branches of saplings, and the influence of the wapiti was significantly greater than that of the Siberian roe deer. This study provides a scientific basis for solving the conservation and management problems of the deer animals foraging on Japanese yew and contributes to further understanding of the competition-coexistence mechanism of sympatric species.

Identifying the processes underlying community assembly and dynamics remains a central goal in ecology. Although much research has been devoted to analyzing how environmental changes affect patterns of trait and species diversity among communities and ecosystems, few studies have resolved the link between fundamental processes, species diversity and trait distributions. It has been suggested that identifying ecological selection on functional traits may provide insight into more general rules of community assembly. In this study, we asked whether and how selection determines species and trait diversity, and how this is determined by the initial community-weighted variance (CWV) and mean (CWM) for traits governing species interactions, as in our case: competitiveness and defense against a predator. We tracked experimental 5-species phytoplankton communities in the presence and absence of a rotifer predator. The communities had at least 3 of the 5 species in common, but differed in CWV and CWM for defense against predation. We found that species diversity was only maintained in the presence of the predator, but that species diversity was highest with higher initial trait distributions and that temporal changes in diversity correlated with trait selection. For low or higher initial distributions, we found early directional selection for defense and competitiveness, followed by reduced selection and an increase in niche availability. For intermediate initial trait distributions, we observed initial directional selection in only one trait followed by stabilizing selection. We attribute changes in selection for defense and competitiveness, and thus species diversity, to changes in predator density, which were more dynamically stable for communities with higher trait diversity. Overall, our results suggest that the initial trait distribution determined species diversity through a feedback loop with changes in selection on traits and predator density.

Bees and moths are globally important pollinators. Xeric barrens in the largely mesic northeastern USA support high levels of pollinator diversity, including rare bees and moths. We investigated the response of bee vs moth communities to abiotic and vegetation drivers in barrens across the region. We sampled environment, vegetation, bees, and moths for 2-4 years in 20 preserves. Employing random forest analysis, we tested the role of 26 abiotic and vegetation predictors of bee vs moth abundance, species richness, Shannon-Wiener Diversity Index, evenness, and species composition. Variables related to climate, canopy cover, and soils were the most important predictors of abundance, diversity, and species composition for both bees and moths. Vegetation variables, such as species richness of shrubs and hostplants, were also important for bees. The direction of these relationships contrasted sharply between bees and moths: bees were more abundant and species rich in more open, sandy sites and moths the opposite. Surprisingly, bee-moth contrasts in diversity did not hold for Shannon-Wiener Diversity. Habitat preferences for a subset of moth xeric specialists were much more similar to bees than to other moths, with a preference for open, sandy conditions. Contrasts between bees and moths in habitat preferences likely stemmed from differences in life history: bees rely on flowers for feeding and porous substrates for nesting, whereas most moth adults rely on flowers but many moth caterpillars use woody plants as hosts. The contrast between bees and moths for species richness vs. Shannon-Wiener Diversity raises important general questions about the conservation value of these two metrics. Our results suggest that, because of differences in habitat preferences among pollinators, barrens management for spatial and temporal heterogeneity is likely to promote the highest abundance and diversity of resident pollinator communities.

1. Widely used methods to assess population genetic structure and differentiation rely on independence of marker loci. Following the assumption, the common metrics, for example FST, evaluate genetic structure by averaging across loci. Common metrics do not use information in the associations among loci at the individual level and are often criticized for failing to measure true differentiation even when loci segregate independently. 2. We introduce a new concept to measure β-variation (Effective Number of Different Populations, ENDP). It requires the following steps: (a) calculation of a proper dissimilarity between genetic profiles of all individuals; (b) calculation of suitable pairwise distances between the samples based on the dissimilarities between individuals; (c) calculation of diversity (in terms of Hill numbers) and dispersion of samples based on the pairwise distances between samples; (d) ENDP is then estimated as a combination of the diversity and dispersion. ENDP estimates β-variation independently of within-sample α-variation. This new concept differs from the existing standard where β-diversity is estimated based on the ‘partition of variation’ scheme (beta=gamma-alpha or beta=gamma/alpha). 3. Estimates of ENDP are obtained by evaluating information in the available genetic profiles of individuals including association of loci. Therefore, ENDP can be used even in an absence of panmixia. 4. We illustrate the use of this concept by analyzing the population genetic structure of a sexual species (a trematode parasite) occupying connected populations across a broad geographic area. Analysis is complicated by two coexisting cryptic sister clades and the potentially mixed-mating system of this hermaphroditic parasite.

Fjord systems in the Norwegian Arctic are experiencing an increasing frequency and magnitude of marine heatwaves. These episodic heat stress events can have varying degrees of acute impacts on primary production and nutrient uptake of mixed kelp communities, as well as modifying the biogeochemical cycling in nearshore systems where vast areas of kelp create structural habitat. To assess the impact of future marine heatwaves on kelp communities, we conducted a 23 d mesocosm experiment exposing mixed kelp communities to warming and heatwave scenarios projected for the year 2100. Three treatments were considered: a constant warming (+1.8C from the control), a medium magnitude and long duration heatwave event (+2.8C from the control for 13 d), and two short-term, more intense, heatwaves (5 d long scenarios with peaks at +3.9C from the control). The results show that both marine heatwave treatments reduced net community production whereas the constant warm temperature treatment displayed no difference from the control. The long marine heatwave scenario resulted in reduced accumulated net community production, indicating that prolonged exposure had a greater severity than two high magnitude, short-term heatwave events. We estimated an 11C temperature threshold at which negative effects to primary production appeared present. We highlight that marine heatwaves can induce sublethal effects on kelp communities by depressing net community production. These results are placed in the context of potential physiological resilience of kelp communities and implications of reduced net community production to future Arctic fjord environmental conditions.

Analyzing the temporal dynamics of ecological communities can shed light on coexistence mechanisms and help understand how populations and communities will behave in the face of climate change. However, little is known about how frog communities respond to climate in urban ecosystems, especially in the Global South. Here, we analyzed how frog species richness and abundance are influenced by microclimate both intra- and inter-annually. We surveyed a peri-urban area in central Brazil, monthly for three years. To test the effect of microclimate on species richness and abundance, we used Generalized Additive Mixed-effects Models. We assessed seasonality using circular statistics. We also tested for differences in temporal beta diversity within and among years by estimating species disappearance and temporal rank shift, in addition to a multivariate model-based method to test the effect of year on species composition. Finally, we tested how taxonomic and phylogenetic alpha diversity changed through time using a novel approach based on Hill numbers. We found that species richness varied little among years and was affected only by photoperiod, while species abundance was more variable both between and within years, being mostly affected by humidity, temperature, and photoperiod. Species composition varied little between years, mostly between the first and subsequent years. Conversely, beta diversity was highest within years. Only the effective taxonomic richness changed significantly through time. Our results help not only understand temporal mechanisms that allow species coexistence, but also allow to make inferences about the impact of urbanization on biodiversity in recently urbanized landscapes, showing that species composition in peri-urban sites remains unaltered in a mid-timescale, especially when climate conditions changes little across years.

Marine sponges are predicted to be winners in the future ocean due to their exemplary adaptive capacity. However, while many sponge groups exhibit tolerance to a wide range of environmental insults, calcifying sponges may be more susceptible to thermo-acidic stress. To describe the gene regulatory networks that govern the stress response of a calcareous sponge, Leucetta chagosensis (class Calcarea, order Clathrinida), individuals were subjected to warming and acidification conditions based on the climate models for 2100. Transcriptome analysis and gene co-expression network reconstruction revealed that the unfolded protein response (UPR) was activated under thermo-acidic stress. Among the upregulated genes were two lineage-specific homologs of X-box binding protein 1 (XBP1), a transcription factor that activates the UPR. Alternative dimerization between these XBP1 gene products suggests a clathrinid-specific mechanism to reversibly sequester the transcription factor into an inactive form, enabling the rapid regulation of pathways linked to the UPR in clathrinid calcareous sponges. Our findings support the idea that transcription factor duplication events may refine evolutionarily conserved molecular pathways and contribute to ecological success.